Manage Lab Websites: Difference between revisions

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== List of Websites ==
== List of Websites ==
* SEA
Last updated on 05/27/2022
* Transportal
* Excipients
* BKSLab
* IrwinLab
* TLDR (formerly known as Tools18)
 
{| class="wikitable"
{| class="wikitable"
|Website
!Website
|Server
!Machine:Port
|Run on
!Run on
!Hosted in (httpd/conf.d)
!Working
|-
|Amis: https://amis.docking.org/
|
|
|Files2 (169.230.75.3)
|Yes
|-
|Arthor: https://arthor.docking.org/
|nun, samekh, n-9-22; Port 8000
|Screen
|Files2 (169.230.75.3)
|Yes
|-
|BKSLab: http://www.bkslab.org/
|gimel:5002
|Supervisord
|Vav (169.230.26.43)
|Yes
|-
|Blaster: https://blaster.docking.org/
|
|
|Vav (169.230.26.43, can not be moved to files2)
|Yes
|-
|Cartblanche: https://cartblanche.docking.org/
|gimel:5066-5067
|
|Files2 (169.230.75.3)
|Yes
|-
|Covalent: http://covalent.docking.org/
|
|
|Vav (169.230.26.43, can not be moved to files2)
|Yes
|-
|DSF: https://dsf.docking.org/
|
|
|Vav (169.230.26.43)
|No (wrong website)
|-
|Duc: https://duc.docking.org/
|
|
|Vav (169.230.26.43)
|No
|-
|Dud: https://dud.docking.org/
|
|
|Vav (169.230.26.43, can not be moved to files2)
|Yes
|-
|Dude18: http://dude18.docking.org/
|
|
|Vav (169.230.26.43)
|No
|-
|Dude: http://dude.docking.org/
|
|
|Vav (169.230.26.43, can not be moved to files2)
|Yes
|-
|-
|BKSLab, IrwinLab
|Dudez: http://dudez.docking.org/
|gimel
|
|
|Files2 (169.230.75.3)
|Yes
|-
|Excipients: http://excipients.docking.org/
|gimel:8093
|Supervisord
|Supervisord
|Vav (169.230.26.43)
|Yes
|-
|Gitlab: https://gitlab.docking.org/
|
|
|Files2 (169.230.75.3)
|No
|-
|HG: https://hg.docking.org/
|
|
|Files2 (169.230.75.3)
|No
|-
|-
|Excipients, TLDR
|IrwinLab: http://irwinlab.compbio.ucsf.edu/
|gimel2
|gimel:5004
|Supervisord
|Supervisord
|Vav (169.230.26.43)
|Yes
|-
|Khanh: http://khanh.docking.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|Metabolite: http://metabolite.docking.org/
|
|
|Tau (169.230.26.43, can not be moved to files2)
|showing wrong website
|-
|Deepchemworkshop: http://deepchemworkshop.docking.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|Prices: http://prices.docking.org/
|gimel:5022
|
|Tau (169.230.26.43)
|No
|-
|Psicquic: http://psicquic.docking.org/
|
|
|Tau (169.230.26.43)
|Yes (broken???)
|-
|Reactor: http://reactor.docking.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|Transporters: http://transporters.ucsf.bkslab.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|Sea16: http://sea16.docking.org/
|gimel:8086
|
|Files2 (169.230.75.3)
|Yes
|-
|SEC: http://sec.docking.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|Smallworld Public: http://sw.docking.org/
|abacus:5020
|screen
|Files2 (169.230.75.3)
|Yes
|-
|Smallworld Private: http://swp.docking.org/
|abacus:8080
|screen
|Files2 (169.230.75.3)
|Yes
|-
|-
|Transportal
|Smallworld Super Private: http://swc.docking.org/
|omega
|abacus:5099
|screen
|screen
|Files2 (169.230.75.3)
|Yes
|-
|Stats: http://stats.docking.org/
|
|
|Vav (169.230.26.43, can not be moved to files2)
|No
|-
|Symp: http://symp.docking.org/
|
|
|Vav (169.230.26.43)
|No
|-
|TLDR http://tldr.docking.org/
|gimel2:5000
|Supervisord
|Files2 (169.230.26.43)
|Yes
|-
|Tool-Selector: http://tool-selector.ucsf.bkslab.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|-
|SEA
|Transportal: http://transportal.docking.org/
|gimel2
|n-9-23 : port 8123
|screen
|screen
|Vav (169.230.26.43)
|Yes
|-
|Upload: http://upload.docking.org/
|
|
|Tau (169.230.26.43)
|Yes
|-
|Zinc12: http://zinc12.docking.org/
|
|
|Tau (169.230.26.43, can not be moved to files2)
|Yes
|-
|-
|Zinc15: http://zinc.docking.org/
|
|
|Files2 (169.230.75.3)
|Yes
|-
|Zinc20: http://zinc20.docking.org/
|
|
|Files2 (169.230.75.3)
|Yes
|-
|-
|}
|}


== Restart Instructions ==
== Restart Instructions after UPS==
 
=== ZINC ===
==== ZINC15 ====
login to n-9-23 and become www
$ screen -r zinc-15
$ cd /mnt/nfs/soft/www/apps/zinc15/envs/
$ source production/bin/activate.csh
$ cd /nfs/soft/www/apps/zinc15/envs/production/bin/
$ sh ./zincserver.restart-backend.sh
 
==== ZINC20 ====
log into n-9-22 and become www
$ screen -r zinc20prod
$ bash
$ source source /mnt/nfs/home/devtest/anaconda3/bin/activate
$ conda activate /nfs/soft/www/apps/zinc21/envs/development
$ cd /nfs/soft/www/apps/zinc21/envs/development/bin/
$ sh ./zincserver.restart-backend.sh
 
=== For websites running on Screen ===
 
==== SEA ====
SEA is running on a screen on gimel
 
Become www on gimel
$ cd /nfs/soft/www/apps/seadev/
On bash shell
$ source tools/anaconda2/bin/activate sea16
$ cd work/seaware/seaware-academic
$ make SEAserver-stop-devel
$ make all
$ make SEAserver-start-devel
Ctrl A+D to detach screen
 
==== Transportal ====
Login n-9-23 and become www
$ screen -ls
$ screen -r transportal
$ cd  /mnt/nfs/soft/www/apps/transportal/
$ source envs/production-3.6/bin/activate.csh
$ cd /nfs/soft/www/home/apps/transportal/src/transportal_2022/transportal
$ python manage.py runserver 0.0.0.0:8123
Ctrl A+D to detach screen
 
=== For websites running on Supervisord ===
==== Restart applications ====
* Become root on server the website runs on gimel
$ supervisorctl status //to list all of current running apps
$ supervisorctl restart <name>
  i.e
$ supervisorctl restart bks-lab
 
<b>TLDR</b> is running on gimel2 and managed by supervisord
$ supervisorctl restart tldr
==== Start Supervisord ====
$ supervisord
 
[[Category : Sysadmin]] [[Category : Khanh]]

Revision as of 20:41, 11 October 2022

List of Websites

Last updated on 05/27/2022

Website Machine:Port Run on Hosted in (httpd/conf.d) Working
Amis: https://amis.docking.org/ Files2 (169.230.75.3) Yes
Arthor: https://arthor.docking.org/ nun, samekh, n-9-22; Port 8000 Screen Files2 (169.230.75.3) Yes
BKSLab: http://www.bkslab.org/ gimel:5002 Supervisord Vav (169.230.26.43) Yes
Blaster: https://blaster.docking.org/ Vav (169.230.26.43, can not be moved to files2) Yes
Cartblanche: https://cartblanche.docking.org/ gimel:5066-5067 Files2 (169.230.75.3) Yes
Covalent: http://covalent.docking.org/ Vav (169.230.26.43, can not be moved to files2) Yes
DSF: https://dsf.docking.org/ Vav (169.230.26.43) No (wrong website)
Duc: https://duc.docking.org/ Vav (169.230.26.43) No
Dud: https://dud.docking.org/ Vav (169.230.26.43, can not be moved to files2) Yes
Dude18: http://dude18.docking.org/ Vav (169.230.26.43) No
Dude: http://dude.docking.org/ Vav (169.230.26.43, can not be moved to files2) Yes
Dudez: http://dudez.docking.org/ Files2 (169.230.75.3) Yes
Excipients: http://excipients.docking.org/ gimel:8093 Supervisord Vav (169.230.26.43) Yes
Gitlab: https://gitlab.docking.org/ Files2 (169.230.75.3) No
HG: https://hg.docking.org/ Files2 (169.230.75.3) No
IrwinLab: http://irwinlab.compbio.ucsf.edu/ gimel:5004 Supervisord Vav (169.230.26.43) Yes
Khanh: http://khanh.docking.org/ Vav (169.230.26.43) Yes
Metabolite: http://metabolite.docking.org/ Tau (169.230.26.43, can not be moved to files2) showing wrong website
Deepchemworkshop: http://deepchemworkshop.docking.org/ Vav (169.230.26.43) Yes
Prices: http://prices.docking.org/ gimel:5022 Tau (169.230.26.43) No
Psicquic: http://psicquic.docking.org/ Tau (169.230.26.43) Yes (broken???)
Reactor: http://reactor.docking.org/ Vav (169.230.26.43) Yes
Transporters: http://transporters.ucsf.bkslab.org/ Vav (169.230.26.43) Yes
Sea16: http://sea16.docking.org/ gimel:8086 Files2 (169.230.75.3) Yes
SEC: http://sec.docking.org/ Vav (169.230.26.43) Yes
Smallworld Public: http://sw.docking.org/ abacus:5020 screen Files2 (169.230.75.3) Yes
Smallworld Private: http://swp.docking.org/ abacus:8080 screen Files2 (169.230.75.3) Yes
Smallworld Super Private: http://swc.docking.org/ abacus:5099 screen Files2 (169.230.75.3) Yes
Stats: http://stats.docking.org/ Vav (169.230.26.43, can not be moved to files2) No
Symp: http://symp.docking.org/ Vav (169.230.26.43) No
TLDR http://tldr.docking.org/ gimel2:5000 Supervisord Files2 (169.230.26.43) Yes
Tool-Selector: http://tool-selector.ucsf.bkslab.org/ Vav (169.230.26.43) Yes
Transportal: http://transportal.docking.org/ n-9-23 : port 8123 screen Vav (169.230.26.43) Yes
Upload: http://upload.docking.org/ Tau (169.230.26.43) Yes
Zinc12: http://zinc12.docking.org/ Tau (169.230.26.43, can not be moved to files2) Yes
Zinc15: http://zinc.docking.org/ Files2 (169.230.75.3) Yes
Zinc20: http://zinc20.docking.org/ Files2 (169.230.75.3) Yes

Restart Instructions after UPS

ZINC

ZINC15

login to n-9-23 and become www 

$ screen -r zinc-15
$ cd /mnt/nfs/soft/www/apps/zinc15/envs/
$ source production/bin/activate.csh
$ cd /nfs/soft/www/apps/zinc15/envs/production/bin/
$ sh ./zincserver.restart-backend.sh

ZINC20

log into n-9-22 and become www 

$ screen -r zinc20prod
$ bash
$ source source /mnt/nfs/home/devtest/anaconda3/bin/activate 
$ conda activate /nfs/soft/www/apps/zinc21/envs/development
$ cd /nfs/soft/www/apps/zinc21/envs/development/bin/
$ sh ./zincserver.restart-backend.sh

For websites running on Screen

SEA

SEA is running on a screen on gimel

Become www on gimel 

$ cd /nfs/soft/www/apps/seadev/
On bash shell
$ source tools/anaconda2/bin/activate sea16
$ cd work/seaware/seaware-academic
$ make SEAserver-stop-devel
$ make all
$ make SEAserver-start-devel
Ctrl A+D to detach screen

Transportal

Login n-9-23 and become www 

$ screen -ls
$ screen -r transportal
$ cd  /mnt/nfs/soft/www/apps/transportal/
$ source envs/production-3.6/bin/activate.csh
$ cd /nfs/soft/www/home/apps/transportal/src/transportal_2022/transportal
$ python manage.py runserver 0.0.0.0:8123
Ctrl A+D to detach screen

For websites running on Supervisord

Restart applications

  • Become root on server the website runs on gimel
$ supervisorctl status //to list all of current running apps
$ supervisorctl restart <name>
  i.e 
$ supervisorctl restart bks-lab

TLDR is running on gimel2 and managed by supervisord 

$ supervisorctl restart tldr

Start Supervisord

$ supervisord
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